Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis

Authors

  • SYAMSUL BAHRI SYAMSUL BAHRI
  • ARIS TRI WAHYUDI
  • NISA RACHMANIA MUBARIK

DOI:

https://doi.org/10.5454/mi.3.1.2

Keywords:

Bacillus sp., plant-growth promoting rhizobacteria, 16S rDNA, ARDRA, genetic diversity

Abstract

Plant-growth promoting rhizobacteria (PGPR) are rhizosphere associated soil-borne bacteria that can enhance plant growth and inhibit the development of root pathogens. Many soil bacteria have been used as PGPR, and one of them is Bacillus sp. The implementation of PGPR is constrained by genotype fluctuation that makes it inactive on the rhizosphere. Our previous study had characterized and revealed that 11 Bacillus sp. isolated from the soybean plant rhizosphere were PGPR. To asses and compare the genetic diversity of these isolates, Amplified Ribosomal DNA Restriction Analysis (ARDRA) and DNA sequence analysis of 16S rRNA were conducted. The construction of Neighbor-joining trees and bootstrap analysis of 100 resamples of ARDRA and 16S rRNA gene sequences were performed using Treecon software for windows ver. 1.3b. ARDRA analysis was done by using four restriction enzymes (RsaI, HaeIII, CfrI and HinfI), resulting in four phylotypes, respectively phylotype I (Bacillus sp. Cr24, Cr33, Cr64 and Cr68), phylotype II (Bacillus sp. Cr 31 and Cr66), phylotype III (Bacillus sp. Cr44 and Cr71) and phylotype IV (Bacillus sp. Cr67, Cr28 and Cr69). Results of BLASTN from 16S rRNA gene sequences showed that these isolates are genetically diversed. The evolution relationship of Bacillus sp. could be shown by the 16S rRNA gene sequences analysis, while ARDRA based on the digestion sites showed their variability.

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How to Cite

SYAMSUL BAHRI, S. B., WAHYUDI, A. T., & MUBARIK, N. R. (2010). Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis. Microbiology Indonesia, 3(1), 2. https://doi.org/10.5454/mi.3.1.2

Issue

Vol. 3 No. 1 (2009): April 2009

Section

Articles 
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                                                      SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[4], , null, null, 500, 1) % line  194, file: SubmissionSearch.inc.php
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                                                SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[3], null, null, null, 500, 1) % line  132, file: SubmissionSearch.inc.php
                                             SubmissionSearch._getMergedArray(Object:Journal, Array[1], null, null) % line  263, file: SubmissionSearch.inc.php
                                          SubmissionSearch.retrieveResults(Object:Request, Object:Journal, Array[1], null, null, null, Object:DBResultRange, Array[1]) % line   92, file: RecommendBySimilarityPlugin.inc.php
                                       RecommendBySimilarityPlugin.callbackTemplateArticlePageFooter(Templates::Article::Footer::PageFooter, Array[3]) % line  107, file: HookRegistry.inc.php
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                              content_6082325297a527_48332634(Object:Smarty_Internal_Template) % line  123, file: smarty_template_resource_base.php
                           Smarty_Template_Resource_Base.getRenderedTemplateCode(Object:Smarty_Internal_Template) % line  114, file: smarty_template_compiled.php
                        Smarty_Template_Compiled.render(Object:Smarty_Internal_Template) % line  216, file: smarty_internal_template.php
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            PKPTemplateManager.display(frontend/pages/article.tpl) % line  287, file: ArticleHandler.inc.php
         ArticleHandler.view(Array[1], Object:Request) % line  391, file: PKPRouter.inc.php
      PKPRouter._authorizeInitializeAndCallRequest(Array[2], Object:Request, Array[1], false) % line  231, file: PKPPageRouter.inc.php
   PKPPageRouter.route(Object:Request) % line  143, file: Dispatcher.inc.php
Dispatcher.dispatch(Object:Request) % line  281, file: PKPApplication.inc.php
PKPApplication.execute() % line   68, file: index.php

                                                                  ADOConnection.CacheExecute(3600, SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2]) % line  132, file: DAO.inc.php
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                                                            ArticleSearchDAO.getPhraseResults(Object:Journal, Array[1], null, null, , 500, 1) % line  201, file: SubmissionSearch.inc.php
                                                         SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[1], , null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                      SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[4], , null, null, 500, 1) % line  194, file: SubmissionSearch.inc.php
                                                   SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[4], null, null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[3], null, null, null, 500, 1) % line  132, file: SubmissionSearch.inc.php
                                             SubmissionSearch._getMergedArray(Object:Journal, Array[1], null, null) % line  263, file: SubmissionSearch.inc.php
                                          SubmissionSearch.retrieveResults(Object:Request, Object:Journal, Array[1], null, null, null, Object:DBResultRange, Array[1]) % line   92, file: RecommendBySimilarityPlugin.inc.php
                                       RecommendBySimilarityPlugin.callbackTemplateArticlePageFooter(Templates::Article::Footer::PageFooter, Array[3]) % line  107, file: HookRegistry.inc.php
                                    HookRegistry.call(Templates::Article::Footer::PageFooter, Array[3]) % line 1256, file: PKPTemplateManager.inc.php
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                        Smarty_Template_Compiled.render(Object:Smarty_Internal_Template) % line  216, file: smarty_internal_template.php
                     Smarty_Internal_Template.render(false, 1) % line  232, file: smarty_internal_templatebase.php
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               Smarty_Internal_TemplateBase.display(frontend/pages/article.tpl, null, 42362804174f266c598cdb32c3208fc745b92101, null) % line  924, file: PKPTemplateManager.inc.php
            PKPTemplateManager.display(frontend/pages/article.tpl) % line  287, file: ArticleHandler.inc.php
         ArticleHandler.view(Array[1], Object:Request) % line  391, file: PKPRouter.inc.php
      PKPRouter._authorizeInitializeAndCallRequest(Array[2], Object:Request, Array[1], false) % line  231, file: PKPPageRouter.inc.php
   PKPPageRouter.route(Object:Request) % line  143, file: Dispatcher.inc.php
Dispatcher.dispatch(Object:Request) % line  281, file: PKPApplication.inc.php
PKPApplication.execute() % line   68, file: index.php

                                                                  ADOConnection.CacheExecute(3600, SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2]) % line  132, file: DAO.inc.php
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                                                            ArticleSearchDAO.getPhraseResults(Object:Journal, Array[1], null, null, , 500, 1) % line  201, file: SubmissionSearch.inc.php
                                                         SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[1], , null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                      SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[4], , null, null, 500, 1) % line  194, file: SubmissionSearch.inc.php
                                                   SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[4], null, null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[3], null, null, null, 500, 1) % line  132, file: SubmissionSearch.inc.php
                                             SubmissionSearch._getMergedArray(Object:Journal, Array[1], null, null) % line  263, file: SubmissionSearch.inc.php
                                          SubmissionSearch.retrieveResults(Object:Request, Object:Journal, Array[1], null, null, null, Object:DBResultRange, Array[1]) % line   92, file: RecommendBySimilarityPlugin.inc.php
                                       RecommendBySimilarityPlugin.callbackTemplateArticlePageFooter(Templates::Article::Footer::PageFooter, Array[3]) % line  107, file: HookRegistry.inc.php
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            PKPTemplateManager.display(frontend/pages/article.tpl) % line  287, file: ArticleHandler.inc.php
         ArticleHandler.view(Array[1], Object:Request) % line  391, file: PKPRouter.inc.php
      PKPRouter._authorizeInitializeAndCallRequest(Array[2], Object:Request, Array[1], false) % line  231, file: PKPPageRouter.inc.php
   PKPPageRouter.route(Object:Request) % line  143, file: Dispatcher.inc.php
Dispatcher.dispatch(Object:Request) % line  281, file: PKPApplication.inc.php
PKPApplication.execute() % line   68, file: index.php

                                                                  ADOConnection.CacheExecute(3600, SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2]) % line  132, file: DAO.inc.php
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                                                      SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[4], , null, null, 500, 1) % line  194, file: SubmissionSearch.inc.php
                                                   SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[4], null, null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
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                                             SubmissionSearch._getMergedArray(Object:Journal, Array[1], null, null) % line  263, file: SubmissionSearch.inc.php
                                          SubmissionSearch.retrieveResults(Object:Request, Object:Journal, Array[1], null, null, null, Object:DBResultRange, Array[1]) % line   92, file: RecommendBySimilarityPlugin.inc.php
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                                    HookRegistry.call(Templates::Article::Footer::PageFooter, Array[3]) % line 1256, file: PKPTemplateManager.inc.php
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                        Smarty_Template_Compiled.render(Object:Smarty_Internal_Template) % line  216, file: smarty_internal_template.php
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               Smarty_Internal_TemplateBase.display(frontend/pages/article.tpl, null, 42362804174f266c598cdb32c3208fc745b92101, null) % line  924, file: PKPTemplateManager.inc.php
            PKPTemplateManager.display(frontend/pages/article.tpl) % line  287, file: ArticleHandler.inc.php
         ArticleHandler.view(Array[1], Object:Request) % line  391, file: PKPRouter.inc.php
      PKPRouter._authorizeInitializeAndCallRequest(Array[2], Object:Request, Array[1], false) % line  231, file: PKPPageRouter.inc.php
   PKPPageRouter.route(Object:Request) % line  143, file: Dispatcher.inc.php
Dispatcher.dispatch(Object:Request) % line  281, file: PKPApplication.inc.php
PKPApplication.execute() % line   68, file: index.php

                                                                  ADOConnection.CacheExecute(3600, SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2]) % line  132, file: DAO.inc.php
                                                               DAO.retrieveCached(SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2], 3600) % line   91, file: ArticleSearchDAO.inc.php
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                                                         SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[1], , null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                      SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[4], , null, null, 500, 1) % line  194, file: SubmissionSearch.inc.php
                                                   SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[4], null, null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[3], null, null, null, 500, 1) % line  132, file: SubmissionSearch.inc.php
                                             SubmissionSearch._getMergedArray(Object:Journal, Array[1], null, null) % line  263, file: SubmissionSearch.inc.php
                                          SubmissionSearch.retrieveResults(Object:Request, Object:Journal, Array[1], null, null, null, Object:DBResultRange, Array[1]) % line   92, file: RecommendBySimilarityPlugin.inc.php
                                       RecommendBySimilarityPlugin.callbackTemplateArticlePageFooter(Templates::Article::Footer::PageFooter, Array[3]) % line  107, file: HookRegistry.inc.php
                                    HookRegistry.call(Templates::Article::Footer::PageFooter, Array[3]) % line 1256, file: PKPTemplateManager.inc.php
                                 PKPTemplateManager.smartyCallHook(Array[1], Object:Smarty_Internal_Template) % line   43, file: 42362804174f266c598cdb32c3208fc745b92101^1c372c95cd85572e0fbc9a53d0323a0b229cfc78_0.app.frontendpagesarticle.tpl.php
                              content_6082325297a527_48332634(Object:Smarty_Internal_Template) % line  123, file: smarty_template_resource_base.php
                           Smarty_Template_Resource_Base.getRenderedTemplateCode(Object:Smarty_Internal_Template) % line  114, file: smarty_template_compiled.php
                        Smarty_Template_Compiled.render(Object:Smarty_Internal_Template) % line  216, file: smarty_internal_template.php
                     Smarty_Internal_Template.render(false, 1) % line  232, file: smarty_internal_templatebase.php
                  Smarty_Internal_TemplateBase._execute(Object:Smarty_Internal_Template, null, 42362804174f266c598cdb32c3208fc745b92101, null, 1) % line  134, file: smarty_internal_templatebase.php
               Smarty_Internal_TemplateBase.display(frontend/pages/article.tpl, null, 42362804174f266c598cdb32c3208fc745b92101, null) % line  924, file: PKPTemplateManager.inc.php
            PKPTemplateManager.display(frontend/pages/article.tpl) % line  287, file: ArticleHandler.inc.php
         ArticleHandler.view(Array[1], Object:Request) % line  391, file: PKPRouter.inc.php
      PKPRouter._authorizeInitializeAndCallRequest(Array[2], Object:Request, Array[1], false) % line  231, file: PKPPageRouter.inc.php
   PKPPageRouter.route(Object:Request) % line  143, file: Dispatcher.inc.php
Dispatcher.dispatch(Object:Request) % line  281, file: PKPApplication.inc.php
PKPApplication.execute() % line   68, file: index.php

                                                                  ADOConnection.CacheExecute(3600, SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2]) % line  132, file: DAO.inc.php
                                                               DAO.retrieveCached(SELECT 				o.submission_id, 				MAX(s.context_id) AS journal_id, 				MAX(i.date_published) AS i_pub, 				MAX(p.date_published) A..., Array[2], 3600) % line   91, file: ArticleSearchDAO.inc.php
                                                            ArticleSearchDAO.getPhraseResults(Object:Journal, Array[1], null, null, , 500, 1) % line  201, file: SubmissionSearch.inc.php
                                                         SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[1], , null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                      SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[4], , null, null, 500, 1) % line  194, file: SubmissionSearch.inc.php
                                                   SubmissionSearch._getMergedPhraseResults(Object:Journal, Array[4], null, null, null, 500, 1) % line  146, file: SubmissionSearch.inc.php
                                                SubmissionSearch._getMergedKeywordResults(Object:Journal, Array[3], null, null, null, 500, 1) % line  132, file: SubmissionSearch.inc.php
                                             SubmissionSearch._getMergedArray(Object:Journal, Array[1], null, null) % line  263, file: SubmissionSearch.inc.php
                                          SubmissionSearch.retrieveResults(Object:Request, Object:Journal, Array[1], null, null, null, Object:DBResultRange, Array[1]) % line   92, file: RecommendBySimilarityPlugin.inc.php
                                       RecommendBySimilarityPlugin.callbackTemplateArticlePageFooter(Templates::Article::Footer::PageFooter, Array[3]) % line  107, file: HookRegistry.inc.php
                                    HookRegistry.call(Templates::Article::Footer::PageFooter, Array[3]) % line 1256, file: PKPTemplateManager.inc.php
                                 PKPTemplateManager.smartyCallHook(Array[1], Object:Smarty_Internal_Template) % line   43, file: 42362804174f266c598cdb32c3208fc745b92101^1c372c95cd85572e0fbc9a53d0323a0b229cfc78_0.app.frontendpagesarticle.tpl.php
                              content_6082325297a527_48332634(Object:Smarty_Internal_Template) % line  123, file: smarty_template_resource_base.php
                           Smarty_Template_Resource_Base.getRenderedTemplateCode(Object:Smarty_Internal_Template) % line  114, file: smarty_template_compiled.php
                        Smarty_Template_Compiled.render(Object:Smarty_Internal_Template) % line  216, file: smarty_internal_template.php
                     Smarty_Internal_Template.render(false, 1) % line  232, file: smarty_internal_templatebase.php
                  Smarty_Internal_TemplateBase._execute(Object:Smarty_Internal_Template, null, 42362804174f266c598cdb32c3208fc745b92101, null, 1) % line  134, file: smarty_internal_templatebase.php
               Smarty_Internal_TemplateBase.display(frontend/pages/article.tpl, null, 42362804174f266c598cdb32c3208fc745b92101, null) % line  924, file: PKPTemplateManager.inc.php
            PKPTemplateManager.display(frontend/pages/article.tpl) % line  287, file: ArticleHandler.inc.php
         ArticleHandler.view(Array[1], Object:Request) % line  391, file: PKPRouter.inc.php
      PKPRouter._authorizeInitializeAndCallRequest(Array[2], Object:Request, Array[1], false) % line  231, file: PKPPageRouter.inc.php
   PKPPageRouter.route(Object:Request) % line  143, file: Dispatcher.inc.php
Dispatcher.dispatch(Object:Request) % line  281, file: PKPApplication.inc.php
PKPApplication.execute() % line   68, file: index.php

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